Results 1 to 10 of about 10,955,529 (276)

Sparse and skew hashing of K-mers. [PDF]

Bioinformatics, 2022
Motivation A dictionary of k-mers is a data structure that stores a set of n distinct k-mers and supports membership queries. This data structure is at the hearth of many important tasks in computational biology.
Pibiri GE.
europepmc   +8 more sources

Syncmers are more sensitive than minimizers for selecting conserved k‑mers in biological sequences [PDF]

PeerJ, 2021
Minimizers are widely used to select subsets of fixed-length substrings (k-mers) from biological sequences in applications ranging from read mapping to taxonomy prediction and indexing of large datasets.
Robert Edgar
doaj   +4 more sources

Effects of spaced k-mers on alignment-free genotyping. [PDF]

Bioinformatics, 2023
Motivation Alignment-free, k-mer based genotyping methods are a fast alternative to alignment-based methods and are particularly well suited for genotyping larger cohorts.
Häntze H, Horton P.
europepmc   +4 more sources

Swiftly identifying strongly unique k-mers [PDF]

Algorithms for Molecular Biology
Motivation Short DNA sequences of length k that appear in a single location (e.g., at a single genomic position, in a single species from a larger set of species, etc.) are called unique k-mers.
Jens Zentgraf, Sven Rahmann
doaj   +5 more sources

Revisiting pangenome openness with k-mers

Peer Community Journal, 2022
Pangenomics is the study of related genomes collectively, usually from the same species or closely related taxa. Originally, pangenomes were defined for bacterial species. After the concept was extended to eukaryotic genomes, two definitions of pangenome
Parmigiani, Luca, Wittler, Roland, Stoye, Jens   +2 more
doaj   +3 more sources

Hyper- k -mers: efficient streaming k -mers representation [PDF]

bioRxiv
K-mers have become ubiquitous in modern bioinformatics pipelines. A key factor in their success is the ability to filter out erroneous k-mers by removing those with low abundances.
Igor Martayan, Lucas Robidou, Yoshihiro Shibuya, Antoine Limasset   +3 more
semanticscholar   +3 more sources

The K-mer File Format: a standardized and compact disk representation of sets of k-mers. [PDF]

Bioinformatics, 2022
Summary Bioinformatics applications increasingly rely on ad hoc disk storage of k-mer sets, e.g. for de Bruijn graphs or alignment indexes. Here, we introduce the K-mer File Format as a general lossless framework for storing and manipulating k-mer sets ...
Dufresne Y, Lemane T, Marijon P, Peterlongo P, Rahman A, Kokot M, Medvedev P, Deorowicz S, Chikhi R.   +8 more
europepmc   +4 more sources

A classification model for lncRNA and mRNA based on k-mers and a convolutional neural network [PDF]

BMC Bioinformatics, 2019
Background Long-chain non-coding RNA (lncRNA) is closely related to many biological activities. Since its sequence structure is similar to that of messenger RNA (mRNA), it is difficult to distinguish between the two based only on sequence biometrics ...
Jianghui Wen, Yeshu Liu, Yu Shi, Haoran Huang, Bing Deng, Xinping Xiao   +5 more
doaj   +3 more sources

Mining statistically-solid k-mers for accurate NGS error correction [PDF]

BMC Genomics, 2018
Background NGS data contains many machine-induced errors. The most advanced methods for the error correction heavily depend on the selection of solid k-mers. A solid k-mer is a k-mer frequently occurring in NGS reads.
Liang Zhao, Jin Xie, Lin Bai, Wen Chen, Mingju Wang, Zhonglei Zhang, Yiqi Wang, Zhe Zhao, Jinyan Li   +8 more
doaj   +3 more sources

Estimating the total genome length of a metagenomic sample using k-mers. [PDF]

BMC Genomics, 2019
Metagenomic sequencing is a powerful technology for studying the mixture of microbes or the microbiomes on human and in the environment. One basic task of analyzing metagenomic data is to identify the component genomes in the community.
Hua K, Zhang X.
europepmc   +4 more sources